PDB Short entry for 1LY2
HEADER    IMMUNE SYSTEM                           06-JUN-02   1LY2              
TITLE     CRYSTAL STRUCTURE OF UNLIGANDED HUMAN CD21 SCR1-SCR2 (COMPLEMENT      
TITLE    2 RECEPTOR TYPE 2)                                                     
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: COMPLEMENT RECEPTOR TYPE 2;                                
COMPND   3 CHAIN: A;                                                            
COMPND   4 SYNONYM: CD21; EPSTEIN-BARR VIRUS RECEPTOR;                          
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;                                   
SOURCE   3 ORGANISM_COMMON: HUMAN;                                              
SOURCE   4 ORGANISM_TAXID: 9606;                                                
SOURCE   5 GENE: CR2;                                                           
SOURCE   6 EXPRESSION_SYSTEM: PICHIA PASTORIS;                                  
SOURCE   7 EXPRESSION_SYSTEM_TAXID: 4922;                                       
SOURCE   8 EXPRESSION_SYSTEM_STRAIN: X-33;                                      
SOURCE   9 EXPRESSION_SYSTEM_VECTOR: PICZA (INVITROGEN) SECRETED PROTEIN        
KEYWDS    COMPLEMENT RECEPTOR; EPSTEIN BARR VIRUS; REGULATOR OF COMPLEMENT      
KEYWDS   2 ACTIVATION; SHORT CONSENSUS REPEAT; VIRAL RECEPTOR; COMPLEMENT       
KEYWDS   3 CONTROL PROTEIN, IMMUNE SYSTEM                                       
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    A.E.PROTA,D.R.SAGE,T.STEHLE,J.D.FINGEROTH                             
REVDAT   5   29-JUL-20 1LY2    1       COMPND REMARK SEQADV HETNAM              
REVDAT   5 2                   1       LINK   SITE                              
REVDAT   4   13-JUL-11 1LY2    1       VERSN                                    
REVDAT   3   24-FEB-09 1LY2    1       VERSN                                    
REVDAT   2   23-AUG-02 1LY2    1       JRNL   AUTHOR                            
REVDAT   1   05-JUL-02 1LY2    0                                                
JRNL        AUTH   A.E.PROTA,D.R.SAGE,T.STEHLE,J.D.FINGEROTH                    
JRNL        TITL   THE CRYSTAL STRUCTURE OF HUMAN CD21: IMPLICATIONS FOR        
JRNL        TITL 2 EPSTEIN-BARR VIRUS AND C3D BINDING.                          
JRNL        REF    PROC.NATL.ACAD.SCI.USA        V.  99 10641 2002              
JRNL        REFN                   ISSN 0027-8424                               
JRNL        PMID   12122212                                                     
JRNL        DOI    10.1073/PNAS.162360499                                       
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.80 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR                                               
REMARK   3   AUTHORS     : BRUNGER                                              
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 0.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL                           
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL                           
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : NULL                           
REMARK   3   NUMBER OF REFLECTIONS             : 11265                          
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE            (WORKING SET) : 0.179                           
REMARK   3   FREE R VALUE                     : 0.234                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.000                          
REMARK   3   FREE R VALUE TEST SET COUNT      : 1127                            
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL                            
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL                         
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL                         
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL                         
REMARK   3   BIN R VALUE           (WORKING SET) : NULL                         
REMARK   3   BIN FREE R VALUE                    : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL                         
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL                         
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL                         
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 996                                     
REMARK   3   NUCLEIC ACID ATOMS       : 0                                       
REMARK   3   HETEROGEN ATOMS          : 28                                      
REMARK   3   SOLVENT ATOMS            : 146                                     
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL                           
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : NULL                                                 
REMARK   3    B22 (A**2) : NULL                                                 
REMARK   3    B33 (A**2) : NULL                                                 
REMARK   3    B12 (A**2) : NULL                                                 
REMARK   3    B13 (A**2) : NULL                                                 
REMARK   3    B23 (A**2) : NULL                                                 
REMARK   3                                                                      
REMARK   3  ESTIMATED COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL                            
REMARK   3   ESD FROM SIGMAA              (A) : NULL                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.007                           
REMARK   3   BOND ANGLES            (DEGREES) : 1.340                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL                            
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL                            
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : NULL                                      
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA                
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL                 
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  NCS MODEL : NULL                                                    
REMARK   3                                                                      
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT          
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL                 
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL                 
REMARK   3                                                                      
REMARK   3  PARAMETER FILE  1  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1LY2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-02.                  
REMARK 100 THE DEPOSITION ID IS D_1000016398.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 01-FEB-01                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7.5                                
REMARK 200  NUMBER OF CRYSTALS USED        : 2                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : NSLS                               
REMARK 200  BEAMLINE                       : X25                                
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.05                               
REMARK 200  MONOCHROMATOR                  : WIGGLER                            
REMARK 200  OPTICS                         : WIGGLER                            
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : CUSTOM-MADE                        
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO                              
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK                          
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 11265                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.800                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 30.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : NULL                               
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 88.4                               
REMARK 200  DATA REDUNDANCY                : NULL                               
REMARK 200  R MERGE                    (I) : NULL                               
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : NULL                               
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.90                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 55.8                               
REMARK 200  DATA REDUNDANCY IN SHELL       : NULL                               
REMARK 200  R MERGE FOR SHELL          (I) : NULL                               
REMARK 200  R SYM FOR SHELL            (I) : 0.10000                            
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: AMORE                                                 
REMARK 200 STARTING MODEL: CRYSTAL STRUCTURE OF LIGANDED CD21 (COMPLEX WITH     
REMARK 200  C3D)                                                                
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 50.41                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 7.5, VAPOR DIFFUSION,       
REMARK 280  HANGING DROP AT 298K, TEMPERATURE 298.0K                            
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1                              
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290                                                                      
REMARK 290     WHERE NNN -> OPERATOR NUMBER                                     
REMARK 290           MMM -> TRANSLATION VECTOR                                  
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS                            
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM             
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY                
REMARK 290 RELATED MOLECULES.                                                   
REMARK 290   SMTRY1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 290                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC                         
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A                                     
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
DBREF  1LY2 A    0   129  UNP    P20023   CR2_HUMAN       20    149             
SEQADV 1LY2 GLU A    0  UNP  P20023    GLY    20 CLONING ARTIFACT               
SEQADV 1LY2 ALA A    1  UNP  P20023    ILE    21 CLONING ARTIFACT               
SEQADV 1LY2 ILE A  129  UNP  P20023    VAL   149 CLONING ARTIFACT               
SEQRES   1 A  130  GLU ALA SER CYS GLY SER PRO PRO PRO ILE LEU ASN GLY          
SEQRES   2 A  130  ARG ILE SER TYR TYR SER THR PRO ILE ALA VAL GLY THR          
SEQRES   3 A  130  VAL ILE ARG TYR SER CYS SER GLY THR PHE ARG LEU ILE          
SEQRES   4 A  130  GLY GLU LYS SER LEU LEU CYS ILE THR LYS ASP LYS VAL          
SEQRES   5 A  130  ASP GLY THR TRP ASP LYS PRO ALA PRO LYS CYS GLU TYR          
SEQRES   6 A  130  PHE ASN LYS TYR SER SER CYS PRO GLU PRO ILE VAL PRO          
SEQRES   7 A  130  GLY GLY TYR LYS ILE ARG GLY SER THR PRO TYR ARG HIS          
SEQRES   8 A  130  GLY ASP SER VAL THR PHE ALA CYS LYS THR ASN PHE SER          
SEQRES   9 A  130  MET ASN GLY ASN LYS SER VAL TRP CYS GLN ALA ASN ASN          
SEQRES  10 A  130  MET TRP GLY PRO THR ARG LEU PRO THR CYS VAL SER ILE          
MODRES 1LY2 ASN A  101  ASN  GLYCOSYLATION SITE                                 
MODRES 1LY2 ASN A  107  ASN  GLYCOSYLATION SITE                                 
HET    NAG  A1001      14                                                       
HET    NAG  A1002      14                                                       
HETNAM     NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE                         
FORMUL   2  NAG    2(C8 H15 N O6)                                               
FORMUL   4  HOH   *146(H2 O)                                                    
SHEET    1   A 2 SER A   2  CYS A   3  0                                        
SHEET    2   A 2 ILE A  21  ALA A  22 -1  O  ILE A  21   N  CYS A   3           
SHEET    1   B 4 GLY A  12  ILE A  14  0                                        
SHEET    2   B 4 VAL A  26  CYS A  31 -1  O  SER A  30   N  ARG A  13           
SHEET    3   B 4 SER A  42  ILE A  46 -1  O  LEU A  43   N  ILE A  27           
SHEET    4   B 4 THR A  54  TRP A  55 -1  O  THR A  54   N  ILE A  46           
SHEET    1   C 2 PHE A  35  ILE A  38  0                                        
SHEET    2   C 2 LYS A  61  TYR A  64 -1  O  LYS A  61   N  ILE A  38           
SHEET    1   D 2 SER A  70  CYS A  71  0                                        
SHEET    2   D 2 TYR A  88  ARG A  89 -1  O  TYR A  88   N  CYS A  71           
SHEET    1   E 4 GLY A  79  ARG A  83  0                                        
SHEET    2   E 4 SER A  93  CYS A  98 -1  O  ALA A  97   N  TYR A  80           
SHEET    3   E 4 SER A 109  CYS A 112 -1  O  VAL A 110   N  VAL A  94           
SHEET    4   E 4 TRP A 118  GLY A 119 -1  O  GLY A 119   N  TRP A 111           
SHEET    1   F 2 PHE A 102  ASN A 105  0                                        
SHEET    2   F 2 THR A 125  SER A 128 -1  O  VAL A 127   N  SER A 103           
SSBOND   1 CYS A    3    CYS A   45                          1555   1555  2.04  
SSBOND   2 CYS A   31    CYS A   62                          1555   1555  2.04  
SSBOND   3 CYS A   71    CYS A  112                          1555   1555  2.05  
SSBOND   4 CYS A   98    CYS A  126                          1555   1555  2.05  
LINK         ND2 ASN A 101                 C1  NAG A1001     1555   1555  1.46  
LINK         ND2 ASN A 107                 C1  NAG A1002     1555   1555  1.46  
CISPEP   1 THR A   19    PRO A   20          0        -0.16                     
CISPEP   2 THR A   86    PRO A   87          0        -0.22                     
CISPEP   3 GLY A  119    PRO A  120          0         0.15                     
CRYST1   31.600   33.270   42.110  91.51 111.44 117.81 P 1           1          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      0.031646  0.016692  0.016910        0.00000                         
SCALE2      0.000000  0.033982  0.008369        0.00000                         
SCALE3      0.000000  0.000000  0.026275        0.00000